Egyptian justice officials and police raided offices of 17 civil society organizations on Thursday as part of an investigation into foreign funding of such groups in Egypt, a security source said.

At least two U.S. rights groups -- The National Democratic Institute (NDI) and the International Republican Institute (IRI) -- are being targeted by the operation, a spokeswoman for Human Rights Watch and judicial sources said.

An AFP journalist saw access to the Cairo offices of the NDI being prohibited by members of the security forces, while men were also seen carrying out boxes full of documents.

The United States expressed deep concern and urged Egyptian authorities to immediately halt “harassment” of non-governmental organization staff.

“We are very concerned because this is not appropriate in the current environment,” State Department spokeswoman Victoria Nuland said, adding that senior U.S. officials had been in touch with Egyptian military leaders to express their concern over the raid.

“We call on the Egyptian government to immediately end the harassment of NGO staff, return all property and resolve this issue immediately,” she said.

Nuland said the U.S. ambassador in Cairo, Anne Patterson, raised her concerns with the Egyptian prime minister, and the assistant secretary of state for Near East Affairs, Jeff Feltman, raised the issue with Egypt’s envoy to the U.S.

The operation is targeting the U.S. group National Democratic Institute, according to Heba Morayef of the global rights group HRW, and the Arab Center for the Independence of Justice, its head Nasser Amin told AFP.

“Security forces who said they were from the public prosecutor are raiding our offices as we speak. They are grabbing all the papers and laptops as well,” one person working at NDI, who gave her name as Rawda, told Reuters.

The security source said employees at the offices were not allowed to leave while the searches continued.

The U.S.-funded International Republican Institute (IRI), which was monitoring elections in Egypt, on Thursday sharply criticized the raid on its Cairo offices by Egyptian security services.

“IRI is dismayed and disappointed by these actions,” the Washington-based group said, adding it was all the more surprised it had happened following the popular revolution that toppled president Hosni Mubarak in February.

“IRI has been working with Egyptians since 2005; it is ironic that even during the Mubarak era IRI was not subjected to such aggressive action,” it said.

It said the raid is “confusing” because the government backed by military rulers tasked with steering the country toward democracy had officially asked the group to witness the parliamentary elections.

The Arab Center for the Independence of Justice (ACIJ) was also being investigated, its head Nasser Amin told AFP, as was the Egyptian Budgetary and Human Rights Organization, according to another judicial source.

“Members of the police force and the army entered our organization’s headquarters accompanied by members of the prosecution,” ACIJ’s Amin said.

The head of the Arabic Network for Human Rights Information, Gamal Eid, says an employee trapped inside one of the NGO’s called him to say security forces are removing laptop computers.

The search operations were ordered by the prosecution service “following complaints of the NGOs (non-governmental organizations) receiving foreign support,” a court official said, speaking on condition of anonymity.

Egypt’s military has vowed to investigate how pro-democracy and human rights organizations are funded and has said repeatedly it will not tolerate foreign interference in the country's affairs.

Some Egyptian human rights groups have been at the vanguard of protests demanding that the army, in power since February when President Hosni Mubarak was ousted, hand power swiftly to elected civilians.

Clashes between protesters and soldiers in Cairo this month left 17 people dead.

The army has pledged to step aside by mid-2012.

Political experts said the groups raided on Thursday have taken a neutral political stance, focusing on fostering democracy in Egypt by training members of nascent parties.

“The National Democratic Institute has been training new parties ... in how to participate in elections,” a leading member of a liberal party said on condition of anonymity.

“This has been with the full knowledge of authorities and was not clandestine.”

Presidential hopeful Mohammed ElBaradie on ‎Thursday stated on Twitter that human rights organizations ‎represented “the guardians of nascent freedom.” He added: ‎‎“Efforts to suffocate them will be a major setback and will surely ‎backfire.”‎

In October, Egypt’s justice minister ‎announced that he had commissioned two judges to investigate ‎foreign funding allegations. At the time, the minister said that any ‎organization found guilty of the practice would be charged with ‎‎“betraying Egypt by deliberately promoting political strife.”‎

Since then, several political movements and activist groups ‎have fended off accusations that they had been recipients of unregistered ‎foreign financing, including the prominent April 6 youth movement.‎

A few weeks after the February ouster of former president Hosni ‎Mubarak, the United States Agency for International ‎Development (USAID) allocated some $65 million towards “democratic development” programs in Egypt, Egypt’s daily al-Ahram said according to a report on Thursday.‎

In July, the government of former prime minister Essam Sharaf ‎drew up a fact-finding committee – headed by the justice minister – to ‎investigate charges of foreign funding for unlicensed local and ‎international NGOs. Sharaf’s committee sought to blacklist any ‎NGO or political party found to have requested financial ‎assistance from USAID.‎

It remains unclear, however, whether or not Thursday’s raids ‎were related to the committee’s findings.

The Cairo-based Arabic Network for Human Rights Information ‎‎(ANHRI) issued a statement saying that “the Mubarak regime did not ‎dare undertake such practices prior to the uprising. There is a ‎systematic campaign against these organizations, which was ‎prepared for in advance, while the media paved the way for it a ‎long time ago. The goal of this campaign is clear to everyone, ‎which is to prevent us from exposing the violations and ‎oppressive practices which are still being committed until this ‎moment,” according to al-Ahram report.